I've done my transmission 4 times. The only time it took a ton of effort was when
we didn't properly support the engine.
These days, I usually support the engine on the oil pan gently with a floor jack and few towels on a short piece of 2x4. If you don't support the front of the engine in this way (or similar on the water pump, or jack straps over top:
https://www.ft86club.com/forums/showthread.php?t=135100), you'll really have to fight to get the transmission aligned.
I never had a significant gap when I did it this way. The two assemblies came together with just a bit of light between them (probably 1/4" or less - see picture for actual achieved gap prior to tightening any bolts).
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When you remove the transmission, the engine wants to lean forward over the subframe motor mounts. This causes the rear of the engine to be angled up to the sky. To counteract this, you need to support the weight of the FRONT of the engine. Preferably, you set-up and support the engine BEFORE you remove the transmission, so it preserves the alignment. That will get you straight-and-true to align the transmission back in.
- The transmission actually holds some of the weight of the engine (through the trans mount - if you ever look up this part on the TRD website, notice that they call it the rear motor mount).
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If you're straight-and-true, but still having trouble getting the input shaft to engage with the flywheel: put the transmission into gear and stick the driveshaft back on. Give the shaft a little twist as you push in to get the splines aligned.